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RESEARCH ARTICLES

Cite as: J. Yu et al., Science


10.1126/science.abc6284 (2020).

DNA vaccine protection against SARS-CoV-2 in rhesus


macaques
Jingyou Yu1*, Lisa H. Tostanoski1*, Lauren Peter1*, Noe B. Mercado1*, Katherine McMahan1*, Shant H.
Mahrokhian1*, Joseph P. Nkolola1*, Jinyan Liu1*, Zhenfeng Li1*, Abishek Chandrashekar1*, David R. Martinez2,
Carolin Loos3, Caroline Atyeo3, Stephanie Fischinger3, John S. Burke3, Matthew D. Slein3, Yuezhou Chen4,
Adam Zuiani4, Felipe J. N. Lelis4, Meghan Travers4, Shaghayegh Habibi4, Laurent Pessaint5, Alex Van Ry5,
Kelvin Blade5, Renita Brown5, Anthony Cook5, Brad Finneyfrock5, Alan Dodson5, Elyse Teow5, Jason Velasco5,
Roland Zahn6, Frank Wegmann6, Esther A. Bondzie1, Gabriel Dagotto1, Makda S. Gebre1, Xuan He1, Catherine
Jacob-Dolan1, Marinela Kirilova1, Nicole Kordana1, Zijin Lin1, Lori F. Maxfield1, Felix Nampanya1, Ramya
Nityanandam1, John D. Ventura1, Huahua Wan1, Yongfei Cai7, Bing Chen7,8, Aaron G. Schmidt3,8, Duane R.
Wesemann4,8, Ralph S. Baric2, Galit Alter3,8, Hanne Andersen5, Mark G. Lewis5, Dan H. Barouch1,3,8†

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1
Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA. 2University of North Carolina at Chapel
Hill, Chapel Hill, NC 27599, USA. 3Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA. 4Brigham and Women’s Hospital, Harvard Medical School, Boston,
MA 02115, USA. 5Bioqual, Rockville, MD 20852, USA. 6Janssen Vaccines & Prevention BV, Leiden, Netherlands. 7Children’s Hospital, Boston, MA 02115, USA.
8
Massachusetts Consortium on Pathogen Readiness, Boston, MA 02215, USA.
*These authors contributed equally to this work.
†Corresponding author. Email: dbarouch@bidmc.harvard.edu

The global COVID-19 pandemic caused by the SARS-CoV-2 virus has made the development of a vaccine a
top biomedical priority. In this study, we developed a series of DNA vaccine candidates expressing different
forms of the SARS-CoV-2 Spike (S) protein and evaluated them in 35 rhesus macaques. Vaccinated animals
developed humoral and cellular immune responses, including neutralizing antibody titers comparable to
those found in convalescent humans and macaques infected with SARS-CoV-2. Following vaccination, all
animals were challenged with SARS-CoV-2, and the vaccine encoding the full-length S protein resulted in
>3.1 and >3.7 log10 reductions in median viral loads in bronchoalveolar lavage and nasal mucosa,
respectively, as compared with sham controls. Vaccine-elicited neutralizing antibody titers correlated with
protective efficacy, suggesting an immune correlate of protection. These data demonstrate vaccine
protection against SARS-CoV-2 in nonhuman primates.

The COVID-19 pandemic has made the development of a safe, the transmembrane domain and cytoplasmic tail reflecting
effective, and deployable vaccine a critical global priority (1– the soluble ectodomain (S.dTM) (10), 4) S1 domain with a fol-
8). However, our understanding of immune correlates of pro- don trimerization tag (S1), 5) receptor-binding domain with
tection to SARS-CoV-2 is currently very limited but is essen- a foldon trimerization tag (RBD), and 6) a prefusion stabi-
tial for the development of SARS-CoV-2 vaccines and other lized soluble ectodomain with deletion of the furin cleavage
immunotherapeutic interventions. To facilitate the preclini- site, two proline mutations, and a foldon trimerization tag
cal evaluation of vaccine candidates, we recently developed a (S.dTM.PP) (11–13) (Fig. 1A). Western blot analyses confirmed
rhesus macaque model of SARS-CoV-2 infection (9). In the expression in cell lysates for all the constructs and in culture
present study, we constructed a set of prototype DNA vac- supernatants for the soluble S.dTM and S.dTM.PP constructs
cines expressing various forms of the SARS-CoV-2 Spike (S) (Fig. 1, B and C). Proteolytic cleavage of the secreted protein
protein and assessed their immunogenicity and protective was noted for S.dTM but not S.dTM.PP, presumably due to
efficacy against SARS-CoV-2 viral challenge in rhesus mutation of the furin cleavage site in S.dTM.PP.
macaques. We immunized 35 adult rhesus macaques (6-12 years old)
with DNA vaccines in the following groups: S (N = 4), S.dCT
Construction and immunogenicity of DNA vaccine (N = 4), S.dTM (N = 4), S1 (N = 4), RBD (N = 4), S.dTM.PP (N
candidates = 5), and sham controls (N = 10). Animals received 5 mg DNA
We produced a series of prototype DNA vaccines expressing vaccines by the intramuscular route without adjuvant at
six variants of the SARS-CoV-2 S protein: 1) full-length (S), 2) week 0 and week 3. After the boost immunization at week 5,
deletion of the cytoplasmic tail (S.dCT) (10), 3) deletion of we observed S-specific binding antibodies by ELISA (Fig. 2A)

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and neutralizing antibodies (NAbs) using both a pseudovirus viral RNA in BAL and NS, respectively, in S vaccinated animals
neutralization assay (10) (Fig. 2B) and a live virus neutraliza- compared with sham controls (P = 0.02 and P = 0.04, two-sided
tion assay (14, 15) (Fig. 2C). Two animals had binding anti- Mann-Whitney tests) (fig. S5). Viral RNA assays were con-
bodies at baseline by ELISA, which we speculate might reflect firmed by PFU assays, which similarly showed lower infectious
cross-reactivity of other natural primate coronaviruses. NAb virus titers in S vaccinated animals compared with sham con-
titers measured by the pseudovirus neutralization assay cor- trols (P = 0.04, two-sided Mann-Whitney test) (fig. S5).
related with NAb titers measured by the live virus neutraliza- We speculated that a substantial fraction of viral RNA in
tion assay (P < 0.0001, R = 0.8052, two-sided Spearman rank- BAL and NS following challenge represented input challenge
correlation test; fig. S1). Moreover, NAb titers in the vac- virus, and thus we also assessed levels of subgenomic mRNA
cinated macaques (median titer 74; median titer in the S and (sgmRNA), which is believed to reflect viral replication cellu-
S.dCT groups 170) were comparable in magnitude to NAb ti- lar intermediates that are not packaged into virions and thus
ters in a cohort of 9 convalescent macaques (median titer putative replicating virus in cells (18). High levels of sgmRNA
106) and a cohort of 27 convalescent humans (median titer were observed in the sham controls (Fig. 4A) with a median
93) who had recovered from SARS-CoV-2 infection (Fig. 2D). peak of 5.35 (range 3.97-6.95) log10 sgmRNA copies/ml in BAL
S-specific and RBD-specific antibodies in the vaccinated and a median peak of 6.40 (range 4.91-7.01) log10 sgmRNA

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macaques included diverse subclasses and effector functions, copies/swab in NS. Peak viral loads occurred variably on day
including antibody-dependent neutrophil phagocytosis 1-4 following challenge. Markedly lower levels of sgmRNA
(ADNP), antibody-dependent complement deposition were observed in the vaccine groups (Fig. 4, B and C), includ-
(ADCD), antibody-dependent monocyte cellular phagocytosis ing >3.1 and >3.7 log10 decreases of median peak sgmRNA in
(ADCP), and antibody-dependent NK cell activation (IFN-γ BAL and NS, respectively, in S vaccinated animals compared
secretion, CD107a degranulation, and MIP-1β expression) (16) with sham controls (P = 0.03 and P = 0.01, two-sided Mann-
(Fig. 2E). A trend toward higher ADCD responses was ob- Whitney tests) (Fig. 4D). Reduced levels of sgmRNA were also
served in the S and S.dCT groups, whereas higher NK cell ac- observed in other vaccine groups, including S.dCT, S1, RBD,
tivation was observed in the RBD and S.dTM.PP groups. A and S.dTM.PP, although minimal to no protection was seen
principal component analysis of the functional and biophys- in the S.dTM group, confirming the importance of prefusion
ical antibody features showed overlap of the different vaccine ectodomain stabilization, as reported previously (13). Protec-
groups, with more distinct profiles in the S and RBD groups tion was generally more robust in BAL compared with NS,
(Fig. 2E). particularly for the less immunogenic constructs. A total of 8
We also observed cellular immune responses to pooled S of 25 vaccinated animals exhibited no detectable sgmRNA in
peptides in the majority of vaccinated animals by IFN-γ BAL and NS at any timepoint following challenge.
ELISPOT assays at week 5 (Fig. 3A). Intracellular cytokine
staining assays at week 5 demonstrated induction of S-spe- Immune correlates of vaccine-induced protection
cific IFN-γ+ CD4+ and CD8+ T cell responses, with lower re- The variability in protective efficacy in this study facilitated
sponses induced by the shorter S1 and RBD immunogens an analysis of immune correlates of protection. The log10
(Fig. 3B). S-specific IL-4+ CD4+ and CD8+ T cell responses pseudovirus NAb titer at week 5 inversely correlated with
were marginal (Fig. 3C), suggesting induction of Th1-biased peak log10 sgmRNA in both BAL (P < 0.0001, R = −0.6877,
cellular immune responses. two-sided Spearman rank-correlation test) and NS (P =
0.0199, R = −0.4162) (Fig. 5A). Similarly, the log10 live virus
Protective efficacy against SARS-CoV-2 challenge NAb titer at week 5 inversely correlated with peak log10
At week 6, which was 3 weeks after the boost immunization, sgmRNA levels in both BAL (P < 0.0001, R = −0.7702) and NS
all animals were challenged with 1.2 × 108 VP (1.1 × 104 PFU) (P = 0.1006, R = −0.3360) (Fig. 5B). These data suggest that
SARS-CoV-2, administered as 1 ml by the intranasal (IN) vaccine-elicited serum NAb titers may be immune correlates
route and 1 ml by the intratracheal (IT) route. Following chal- of protection against SARS-CoV-2 challenge. We speculate
lenge, we assessed viral RNA levels by RT-PCR (17) in bron- that correlations were more robust with viral loads in BAL
choalveolar lavage (BAL) and nasal swabs (NS). Viral RNA compared with viral loads in NS due to intrinsic variability of
was negative in plasma, and animals exhibited only mild clin- collecting swabs. The log10 ELISA titer at week 5 also inversely
ical symptoms. High levels of viral RNA were observed in the correlated with peak log10 sgmRNA levels in BAL (P = 0.0041,
sham controls with a median peak of 6.46 (range 4.81-7.99) R = −0.4733) (fig. S6). Vaccine-elicited ELISPOT responses
log10 RNA copies/ml in BAL and a median peak of 6.82 (range (fig. S7), CD4+ ICS responses (fig. S8), and CD8+ ICS re-
5.96-7.96) log10 RNA copies/swab in NS (fig. S2). Lower levels sponses (fig. S9) did not correlate with protection.
of viral RNA were observed in the vaccine groups (figs. S3 and We next explored the potential contribution of other anti-
S4), including 1.92 and 2.16 log10 reductions of median peak body effector functions to immune correlates of protection.

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In addition to NAb titers, S- and RBD-specific ADCD re- was likely not sterilizing but instead appeared to be mediated
sponses inversely correlated with peak log10 sgmRNA levels by rapid immunologic control following challenge.
in BAL (Fig. 5C, top panel). Two orthogonal unbiased ma- Our data extend previous studies on SARS and MERS vac-
chine learning approaches were then utilized to define mini- cine protection in mice, ferrets, and macaques (10, 21–24).
mal combined correlates of protection. A nonlinear random Phase 1 clinical studies for SARS and MERS vaccine candi-
forest regression analysis and a linear partial least squares dates have also been conducted (25), but these vaccines have
regression analysis showed that utilizing two features im- not been tested for efficacy in humans. Our data suggest that
proved the correlations with protection, such as RBD-specific vaccine protection against SARS-CoV-2 in macaques is feasi-
FcγR2a-1 binding with ADCD responses, or NAb titers with ble. We observed a dramatic reduction of viral replication in
RBD-specific IgG2 responses (Fig. 5C, bottom left panel). both the upper respiratory tract and the lower respiratory
Moreover, NAb titers correlated with most antibody effector tract with the optimal vaccines. In contrast, the less immu-
functions, except for antibody-mediated NK cell activation nogenic vaccines, such as S.dTM, showed partial protection
(Fig. 5C, bottom right panel). Taken together, these data sug- in BAL but essentially no protection in NS. These data sug-
gest a primary role of NAbs in protecting against SARS-CoV- gest that it may be easier to protect against lower respiratory
2, supported by certain innate immune effector functions tract disease compared with upper respiratory tract disease.

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such as ADCD. In the present study, optimal protection was achieved with
Finally, we compared antibody parameters in the vac- the full-length S immunogen in both the upper and lower res-
cinated animals that were completely protected (defined as piratory tracts, and reduced protection was observed with
no detectable sgmRNA following challenge) with the vac- soluble constructs and smaller fragments. Our study did not
cinated animals that were partially protected (defined as de- address the question of whether emerging mutations in the
tectable sgmRNA following challenge). Completely protected SARS-CoV-2 S sequence may mediate escape from NAb
animals showed higher log10 NAb titers (P = 0.0004, two- responses induced by immunogens designed from the
sided Mann-Whitney test), RBD-specific ADCD responses (P Wuhan/WIV04/2019 sequence.
= 0.0001), S-specific RBD responses (P = 0.0010), and RBD- Further research will need to address the important ques-
specific ADCP responses (P = 0.0005) compared with par- tions of the durability of protective immunity and the optimal
tially protected animals (Fig. 5D). vaccine platforms for a SARS-CoV-2 vaccine for humans (26).
Although our data are restricted to DNA vaccines, we believe
Anamnestic immune responses following challenge that our findings should be generalizable to other gene-based
All animals exhibited anamnestic humoral and cellular im- vaccines as well, including RNA vaccines and recombinant
mune responses following challenge, including increased vector-based vaccines. Additional research should also evalu-
ELISA titers (fig. S10), pseudovirus NAb titers (fig. S11), live ate vaccine immunogenicity and protective efficacy in older
virus NAb titers (fig. S12), and IFN-γ ELISPOT responses (fig. animals. Further studies will also need to address the ques-
S13) on day 14 after challenge. These data suggest that vac- tion of enhanced respiratory disease, which may result from
cine protection was probably not sterilizing, including in the antibody-dependent enhancement (27–29). Although our
8 of 25 animals that had no detectable sgmRNA in BAL and study was not designed to address safety issues, it is worth
NS at any timepoint following challenge, but rather was likely noting that the DNA vaccines induced Th1 rather than Th2
mediated by rapid virologic control following challenge. responses, and we did not observe enhanced clinical disease
even with the suboptimal vaccine constructs that failed to
Discussion protect.
A safe and effective SARS-CoV-2 vaccine may be required to We identified serum NAb titers, as measured by two inde-
end the global COVID-19 pandemic. Several vaccine candi- pendent assays (pseudovirus neutralization and live virus
dates have initiated clinical testing, and many others are in neutralization), as a significant correlate of protection in this
preclinical development (19, 20). However, very little is cur- study against both lower respiratory tract disease as well as
rently known about immune correlates of protection and pro- upper respiratory tract disease. It is likely that protection in
tective efficacy of candidate SARS-CoV-2 vaccines in animal both anatomic compartments will be necessary for pandemic
models. In this study, we generated a series of prototype DNA control, although protection in the upper respiratory tract
vaccines expressing various S immunogens and assessed pro- may be more difficult to achieve. If this NAb correlate proves
tective efficacy against intranasal and intratracheal SARS- generalizable across multiple vaccine studies in both NHPs
CoV-2 challenge in rhesus macaques. We demonstrate vac- and humans, then this parameter would be a simple and use-
cine protection with substantial >3.1 and >3.7 log10 reductions ful benchmark for clinical development of SARS-CoV-2 vac-
in median viral loads in BAL and NS, respectively, in S im- cines. Innate immune effector functions such as ADCD may
munized animals compared with sham controls. Protection also contribute to protective efficacy. In summary, we

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demonstrate effective vaccine protection against SARS-CoV- human coronavirus spike protein. Nature 531, 118–121 (2016).
2 in rhesus macaques and define NAb titers as an immune doi:10.1038/nature17200 Medline
12. J. Pallesen, N. Wang, K. S. Corbett, D. Wrapp, R. N. Kirchdoerfer, H. L. Turner, C. A.
correlate of protection, which will accelerate the develop- Cottrell, M. M. Becker, L. Wang, W. Shi, W.-P. Kong, E. L. Andres, A. N. Kettenbach,
ment of SARS-CoV-2 vaccines for humans. M. R. Denison, J. D. Chappell, B. S. Graham, A. B. Ward, J. S. McLellan,
Immunogenicity and structures of a rationally designed prefusion MERS-CoV
REFERENCES AND NOTES spike antigen. Proc. Natl. Acad. Sci. U.S.A. 114, E7348–E7357 (2017).
1. F. Wu, S. Zhao, B. Yu, Y.-M. Chen, W. Wang, Z.-G. Song, Y. Hu, Z.-W. Tao, J.-H. Tian, doi:10.1073/pnas.1707304114 Medline
Y.-Y. Pei, M.-L. Yuan, Y.-L. Zhang, F.-H. Dai, Y. Liu, Q.-M. Wang, J.-J. Zheng, L. Xu, 13. D. Wrapp, N. Wang, K. S. Corbett, J. A. Goldsmith, C.-L. Hsieh, O. Abiona, B. S.
E. C. Holmes, Y.-Z. Zhang, A new coronavirus associated with human respiratory Graham, J. S. McLellan, Cryo-EM structure of the 2019-nCoV spike in the
disease in China. Nature 579, 265–269 (2020). doi:10.1038/s41586-020-2008-3 prefusion conformation. Science 367, 1260–1263 (2020).
Medline doi:10.1126/science.abb2507 Medline
2. P. Zhou, X.-L. Yang, X.-G. Wang, B. Hu, L. Zhang, W. Zhang, H.-R. Si, Y. Zhu, B. Li, C.- 14. T. Scobey, B. L. Yount, A. C. Sims, E. F. Donaldson, S. S. Agnihothram, V. D.
L. Huang, H.-D. Chen, J. Chen, Y. Luo, H. Guo, R.-D. Jiang, M.-Q. Liu, Y. Chen, X.-R. Menachery, R. L. Graham, J. Swanstrom, P. F. Bove, J. D. Kim, S. Grego, S. H.
Shen, X. Wang, X.-S. Zheng, K. Zhao, Q.-J. Chen, F. Deng, L.-L. Liu, B. Yan, F.-X. Randell, R. S. Baric, Reverse genetics with a full-length infectious cDNA of the
Zhan, Y.-Y. Wang, G.-F. Xiao, Z.-L. Shi, A pneumonia outbreak associated with a Middle East respiratory syndrome coronavirus. Proc. Natl. Acad. Sci. U.S.A. 110,
new coronavirus of probable bat origin. Nature 579, 270–273 (2020). 16157–16162 (2013). doi:10.1073/pnas.1311542110 Medline
doi:10.1038/s41586-020-2012-7 Medline 15. B. Yount, K. M. Curtis, E. A. Fritz, L. E. Hensley, P. B. Jahrling, E. Prentice, M. R.
3. M. L. Holshue, C. DeBolt, S. Lindquist, K. H. Lofy, J. Wiesman, H. Bruce, C. Spitters, Denison, T. W. Geisbert, R. S. Baric, Reverse genetics with a full-length infectious

Downloaded from http://science.sciencemag.org/ on June 4, 2020


K. Ericson, S. Wilkerson, A. Tural, G. Diaz, A. Cohn, L. Fox, A. Patel, S. I. Gerber, L. cDNA of severe acute respiratory syndrome coronavirus. Proc. Natl. Acad. Sci.
Kim, S. Tong, X. Lu, S. Lindstrom, M. A. Pallansch, W. C. Weldon, H. M. Biggs, T. M. U.S.A. 100, 12995–13000 (2003). doi:10.1073/pnas.1735582100 Medline
Uyeki, S. K. Pillai; Washington State 2019-nCoV Case Investigation Team, First 16. A. W. Chung, M. P. Kumar, K. B. Arnold, W. H. Yu, M. K. Schoen, L. J. Dunphy, T. J.
Case of 2019 Novel Coronavirus in the United States. N. Engl. J. Med. 382, 929– Suscovich, N. Frahm, C. Linde, A. E. Mahan, M. Hoffner, H. Streeck, M. E.
936 (2020). doi:10.1056/NEJMoa2001191 Medline Ackerman, M. J. McElrath, H. Schuitemaker, M. G. Pau, L. R. Baden, J. H. Kim, N.
4. Q. Li, X. Guan, P. Wu, X. Wang, L. Zhou, Y. Tong, R. Ren, K. S. M. Leung, E. H. Y. Lau, L. Michael, D. H. Barouch, D. A. Lauffenburger, G. Alter, Dissecting Polyclonal
J. Y. Wong, X. Xing, N. Xiang, Y. Wu, C. Li, Q. Chen, D. Li, T. Liu, J. Zhao, M. Liu, W. Vaccine-Induced Humoral Immunity against HIV Using Systems Serology. Cell
Tu, C. Chen, L. Jin, R. Yang, Q. Wang, S. Zhou, R. Wang, H. Liu, Y. Luo, Y. Liu, G. 163, 988–998 (2015). doi:10.1016/j.cell.2015.10.027 Medline
Shao, H. Li, Z. Tao, Y. Yang, Z. Deng, B. Liu, Z. Ma, Y. Zhang, G. Shi, T. T. Y. Lam, J. 17. P. Abbink, N. B. Mercado, J. P. Nkolola, R. L. Peterson, H. Tuyishime, K. McMahan,
T. Wu, G. F. Gao, B. J. Cowling, B. Yang, G. M. Leung, Z. Feng, Early Transmission E. T. Moseley, E. N. Borducchi, A. Chandrashekar, E. A. Bondzie, A. Agarwal, A. J.
Dynamics in Wuhan, China, of Novel Coronavirus-Infected Pneumonia. N. Engl. J. Belli, K. A. Reimann, B. F. Keele, R. Geleziunas, M. G. Lewis, D. H. Barouch, Lack of
Med. 382, 1199–1207 (2020). doi:10.1056/NEJMoa2001316 Medline therapeutic efficacy of an antibody to α4β7 in SIVmac251-infected rhesus
5. N. Zhu, D. Zhang, W. Wang, X. Li, B. Yang, J. Song, X. Zhao, B. Huang, W. Shi, R. Lu, macaques. Science 365, 1029–1033 (2019). doi:10.1126/science.aaw8562
P. Niu, F. Zhan, X. Ma, D. Wang, W. Xu, G. Wu, G. F. Gao, W. Tan; China Novel Medline
Coronavirus Investigating and Research Team, A Novel Coronavirus from Patients 18. R. Wölfel, V. M. Corman, W. Guggemos, M. Seilmaier, S. Zange, M. A. Müller, D.
with Pneumonia in China, 2019. N. Engl. J. Med. 382, 727–733 (2020). Niemeyer, T. C. Jones, P. Vollmar, C. Rothe, M. Hoelscher, T. Bleicker, S. Brünink,
doi:10.1056/NEJMoa2001017 Medline J. Schneider, R. Ehmann, K. Zwirglmaier, C. Drosten, C. Wendtner, Virological
6. N. Chen, M. Zhou, X. Dong, J. Qu, F. Gong, Y. Han, Y. Qiu, J. Wang, Y. Liu, Y. Wei, J. assessment of hospitalized patients with COVID-2019. Nature 10.1038/s41586-
Xia, T. Yu, X. Zhang, L. Zhang, Epidemiological and clinical characteristics of 99 020-2196-x (2020). doi:10.1038/s41586-020-2196-x Medline
cases of 2019 novel coronavirus pneumonia in Wuhan, China: A descriptive study. 19. Q. Gao, L. Bao, H. Mao, L. Wang, K. Xu, M. Yang, Y. Li, L. Zhu, N. Wang, Z. Lv, H. Gao,
Lancet 395, 507–513 (2020). doi:10.1016/S0140-6736(20)30211-7 Medline X. Ge, B. Kan, Y. Hu, J. Liu, F. Cai, D. Jiang, Y. Yin, C. Qin, J. Li, X. Gong, X. Lou, W.
7. C. Huang, Y. Wang, X. Li, L. Ren, J. Zhao, Y. Hu, L. Zhang, G. Fan, J. Xu, X. Gu, Z. Shi, D. Wu, H. Zhang, L. Zhu, W. Deng, Y. Li, J. Lu, C. Li, X. Wang, W. Yin, Y. Zhang,
Cheng, T. Yu, J. Xia, Y. Wei, W. Wu, X. Xie, W. Yin, H. Li, M. Liu, Y. Xiao, H. Gao, L. C. Qin, Development of an inactivated vaccine candidate for SARS-CoV-2. Science
Guo, J. Xie, G. Wang, R. Jiang, Z. Gao, Q. Jin, J. Wang, B. Cao, Clinical features of 10.1126/science.abc1932 (2020). doi:10.1126/science.abc1932 Medline
patients infected with 2019 novel coronavirus in Wuhan, China. Lancet 395, 497– 20. B. L. Corey, J. R. Mascola, A. S. Fauci, F. S. Collins, A strategic approach to COVID-
506 (2020). doi:10.1016/S0140-6736(20)30183-5 Medline 19 vaccine R&D. Science 10.1126/science.abc5312 (2020).
8. J. F. Chan, S. Yuan, K.-H. Kok, K. K.-W. To, H. Chu, J. Yang, F. Xing, J. Liu, C. C.-Y. doi:10.1126/science.abc5312 Medline
Yip, R. W.-S. Poon, H.-W. Tsoi, S. K.-F. Lo, K.-H. Chan, V. K.-M. Poon, W.-M. Chan, 21. R. Liu, J. Wang, Y. Shao, X. Wang, H. Zhang, L. Shuai, J. Ge, Z. Wen, Z. Bu, A
J. D. Ip, J.-P. Cai, V. C.-C. Cheng, H. Chen, C. K.-M. Hui, K.-Y. Yuen, A familial cluster recombinant VSV-vectored MERS-CoV vaccine induces neutralizing antibody and
of pneumonia associated with the 2019 novel coronavirus indicating person-to- T cell responses in rhesus monkeys after single dose immunization. Antiviral Res.
person transmission: A study of a family cluster. Lancet 395, 514–523 (2020). 150, 30–38 (2018). doi:10.1016/j.antiviral.2017.12.007 Medline
doi:10.1016/S0140-6736(20)30154-9 Medline 22. K. Muthumani, D. Falzarano, E. L. Reuschel, C. Tingey, S. Flingai, D. O. Villarreal, M.
9. A. Chandrashekar, J. Liu, A. J. Martinot, K. McMahan, N. B. Mercado, L. Peter, L. H. Wise, A. Patel, A. Izmirly, A. Aljuaid, A. M. Seliga, G. Soule, M. Morrow, K. A.
Tostanoski, J. Yu, Z. Maliga, M. Nekorchuk, K. Busman-Sahay, M. Terry, L. M. Kraynyak, A. S. Khan, D. P. Scott, F. Feldmann, R. LaCasse, K. Meade-White, A.
Wrijil, S. Ducat, D. R. Martinez, C. Atyeo, S. Fischinger, J. S. Burke, M. D. Slein, L. Okumura, K. E. Ugen, N. Y. Sardesai, J. J. Kim, G. Kobinger, H. Feldmann, D. B.
Pessaint, A. Van Ry, J. Greenhouse, T. Taylor, K. Blade, A. Cook, B. Finneyfrock, R. Weiner, A synthetic consensus anti–spike protein DNA vaccine induces protective
Brown, E. Teow, J. Velasco, R. Zahn, F. Wegmann, P. Abbink, E. A. Bondzie, G. immunity against Middle East respiratory syndrome coronavirus in nonhuman
Dagotto, M. S. Gebre, X. He, C. Jacob-Dolan, N. Kordana, Z. Li, M. A. Lifton, S. H. primates. Sci. Transl. Med. 7, 301ra132 (2015). doi:10.1126/scitranslmed.aac7462
Mahrokhian, L. F. Maxfield, R. Nityanandam, J. P. Nkolola, A. G. Schmidt, A. D. Medline
Miller, R. S. Baric, G. Alter, P. K. Sorger, J. D. Estes, H. Andersen, M. G. Lewis, D. H. 23. G. P. Kobinger, J. M. Figueredo, T. Rowe, Y. Zhi, G. Gao, J. C. Sanmiguel, P. Bell, N.
Barouch, SARS-CoV-2 infection protects against rechallenge in rhesus macaques. A. Wivel, L. A. Zitzow, D. B. Flieder, R. J. Hogan, J. M. Wilson, Adenovirus-based
Science 10.1126/science.abc4776 (2020). doi:10.1126/science.abc4776 vaccine prevents pneumonia in ferrets challenged with the SARS coronavirus and
10. Z. Y. Yang, W. P. Kong, Y. Huang, A. Roberts, B. R. Murphy, K. Subbarao, G. J. Nabel, stimulates robust immune responses in macaques. Vaccine 25, 5220–5231
A DNA vaccine induces SARS coronavirus neutralization and protective immunity (2007). doi:10.1016/j.vaccine.2007.04.065 Medline
in mice. Nature 428, 561–564 (2004). doi:10.1038/nature02463 Medline 24. J. Zhou, W. Wang, Q. Zhong, W. Hou, Z. Yang, S.-Y. Xiao, R. Zhu, Z. Tang, Y. Wang,
11. R. N. Kirchdoerfer, C. A. Cottrell, N. Wang, J. Pallesen, H. M. Yassine, H. L. Turner, Q. Xian, H. Tang, L. Wen, Immunogenicity, safety, and protective efficacy of an
K. S. Corbett, B. S. Graham, J. S. McLellan, A. B. Ward, Pre-fusion structure of a

First release: 20 May 2020 www.sciencemag.org (Page numbers not final at time of first release) 4
inactivated SARS-associated coronavirus vaccine in rhesus monkeys. Vaccine 23, SUPPLEMENTARY MATERIALS
3202–3209 (2005). doi:10.1016/j.vaccine.2004.11.075 Medline science.sciencemag.org/cgi/content/full/science.abc6284/DC1
25. J. E. Martin, M. K. Louder, L. A. Holman, I. J. Gordon, M. E. Enama, B. D. Larkin, C. Materials and Methods
A. Andrews, L. Vogel, R. A. Koup, M. Roederer, R. T. Bailer, P. L. Gomez, M. Nason, Figs. S1 to S13
J. R. Mascola, G. J. Nabel, B. S. Graham; VRC 301 Study Team, A SARS DNA References
vaccine induces neutralizing antibody and cellular immune responses in healthy
adults in a Phase I clinical trial. Vaccine 26, 6338–6343 (2008). 5 May 2020; accepted 16 May 2020
doi:10.1016/j.vaccine.2008.09.026 Medline Published online 20 May 2020
26. P. Abbink, R. A. Larocca, K. Visitsunthorn, M. Boyd, R. A. De La Barrera, G. D. 10.1126/science.abc6284
Gromowski, M. Kirilova, R. Peterson, Z. Li, O. Nanayakkara, R. Nityanandam, N. B.
Mercado, E. N. Borducchi, A. Chandrashekar, D. Jetton, S. Mojta, P. Gandhi, J.
LeSuer, S. Khatiwada, M. G. Lewis, K. Modjarrad, R. G. Jarman, K. H. Eckels, S. J.
Thomas, N. L. Michael, D. H. Barouch, Durability and correlates of vaccine
protection against Zika virus in rhesus monkeys. Sci. Transl. Med. 9, eaao4163
(2017). doi:10.1126/scitranslmed.aao4163 Medline
27. C. T. Tseng, E. Sbrana, N. Iwata-Yoshikawa, P. C. Newman, T. Garron, R. L. Atmar,
C. J. Peters, R. B. Couch, Immunization with SARS coronavirus vaccines leads to
pulmonary immunopathology on challenge with the SARS virus. PLOS ONE 7,
e35421 (2012). doi:10.1371/journal.pone.0035421 Medline

Downloaded from http://science.sciencemag.org/ on June 4, 2020


28. L. Liu, Q. Wei, Q. Lin, J. Fang, H. Wang, H. Kwok, H. Tang, K. Nishiura, J. Peng, Z.
Tan, T. Wu, K.-W. Cheung, K.-H. Chan, X. Alvarez, C. Qin, A. Lackner, S. Perlman,
K.-Y. Yuen, Z. Chen, Anti-spike IgG causes severe acute lung injury by skewing
macrophage responses during acute SARS-CoV infection. JCI Insight 4, e123158
(2019). doi:10.1172/jci.insight.123158 Medline
29. B. S. Graham, Rapid COVID-19 vaccine development. Science
10.1126/science.abb8923 (2020). doi:10.1126/science.abb8923 Medline
ACKNOWLEDGMENTS
We thank D. Lauffenburger, T. Orekov, A. Thomas, M. Porto, N. Thornburg, P. Abbink,
E. Borducchi, M. Silva, A. Richardson, C. Caron, and J. Cwiak for generous advice,
assistance, and reagents. Funding: We acknowledge support from the Ragon
Institute of MGH, MIT, and Harvard, Mark and Lisa Schwartz Foundation, Beth
Israel Deaconess Medical Center, Massachusetts Consortium on Pathogen
Readiness (MassCPR), Janssen Vaccines & Prevention BV, and the National
Institutes of Health (OD024917, AI129797, AI124377, AI128751, AI126603 to
D.H.B.; AI007151 to D.R.M.; AI146779 to A.G.S.; AI121394, AI139538 to D.R.W.;
272201700036I-0-759301900131-1, AI100625, AI110700, AI132178, AI149644,
AI108197 to R.S.B.). We also acknowledge a Burroughs Wellcome Fund
Postdoctoral Enrichment Program Award to D.R.M. Author contributions:
D.H.B. designed the study. J.Y., L.H.T., L.P., N.B.M., K.M., S.H.M., J.P.N., J.L.,
Z.L., A.C., E.A.B., G.D., M.S.G., X.H., C.J.D., M.K., N.K., Z.L., L.F.M., F.N., R.N., J.V.,
and H.W. performed the immunologic and virologic assays. D.R.M. and R.S.B.
performed the live virus neutralization assays. C.L., C.A., S.F., J.S.B., M.D.S., and
G.A. performed the systems serology. Y.C., A.Z., F.J.N.L., M.T., S.H., and D.R.W.
provided the convalescent human specimens. L.P., A.V.R., K.B., R.B., A.C., B.F.,
A.D., E.T., J.D.V., H.A., and M.G.L. led the clinical care of the animals. R.Z. and
F.W. participated in study design and interpretation of data. Y.C., B.C., and A.G.S.
provided purified proteins. D.H.B., J.L., Z.L., and B.C. designed the immunogens.
D.H.B. wrote the paper with all co-authors. Competing interests: The authors
declare no competing financial interests. D.H.B. is a co-inventor on related
vaccine patents. R.Z. and F.W. are employees of Janssen Vaccines & Prevention
BV. Data and materials availability: All data are available in the manuscript or
the supplementary materials. Correspondence and requests for materials should
be addressed to D.H.B. (dbarouch@bidmc.harvard.edu). This work is licensed
under a Creative Commons Attribution 4.0 International (CC BY 4.0) license,
which permits unrestricted use, distribution, and reproduction in any medium,
provided the original work is properly cited. To view a copy of this license, visit
https://creativecommons.org/licenses/by/4.0/. This license does not apply to
figures/photos/artwork or other content included in the article that is credited
to a third party; obtain authorization from the rights holder before using such
material.

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Fig. 1. Construction of candidate DNA vaccines against SARS-CoV-2.
(A) Six DNA vaccines were produced expressing different SARS-CoV-2
Spike (S) variants: 1) full-length (S), 2) deletion of the cytoplasmic tail
(S.dCT), 3) deletion of the transmembrane domain and cytoplasmic tail
reflecting the soluble ectodomain (S.dTM), 4) S1 domain with a foldon
trimerization tag (S1), 5) receptor-binding domain with a foldon
trimerization tag (RBD), and a 6) prefusion stabilized soluble
ectodomain with deletion of the furin cleavage site, two proline
mutations, and a foldon trimerization tag (S.dTM.PP). Open square
depicts foldon trimerization tag; red lines depict proline mutations. (B)
Western blot analyses for expression from DNA vaccines encoding S
(lane 1), S.dCT (lane 2), S.dTM (lane 3), and S.dTM.PP (lane 4) in cell
lysates and culture supernatants using an anti-SARS polyclonal antibody
(BEI Resources). (C) Western blot analyses for expression from DNA
vaccines encoding S1 (lane 1) and RBD (lane 2) in cell lysates using an
anti-SARS-CoV-2 RBD polyclonal antibody (Sino Biological).

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Fig. 2. Humoral immune responses in vaccinated rhesus macaques. Humoral immune responses were assessed
following immunization by (A) binding antibody ELISA, (B) pseudovirus neutralization assays, and (C) live virus
neutralization assays. (D) Comparison of pseudovirus neutralization titers in vaccinated macaques (all animals and S
/ S.dCT groups), a cohort of 9 convalescent macaques, and a cohort of 27 convalescent humans from Boston, United
States who had recovered from SARS-CoV-2 infection. (E) S- and RBD-specific antibody-dependent neutrophil
phagocytosis (ADNP), antibody-dependent complement deposition (ADCD), antibody-dependent monocyte cellular
phagocytosis (ADCP), and antibody-dependent NK cell activation (IFN-γ secretion, CD107a degranulation, and MIP-1β
expression) are shown. Radar plots show the distribution of antibody features across the vaccine groups. The size and
color intensity of the wedges indicate the median of the feature for the corresponding group (blue depicts antibody
functions, red depicts antibody isotype/subclass/FcγR binding). The principal component analysis (PCA) plot shows
the multivariate antibody profiles across groups. Each dot represents an animal, the color of the dot denotes the group,
and the ellipses shows the distribution of the groups as 70% confidence levels assuming a multivariate normal
distribution. Red bars reflect median responses. Dotted lines reflect assay limit of detection.

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Fig. 3. Cellular immune responses in vaccinated rhesus macaques. Cellular immune responses were
assessed at week 5 following immunization by (A) IFN-γ ELISPOT assays and (B) IFN-γ+ and (C) IL-4+
intracellular cytokine staining assays for CD4+ and CD8+ T cells in response to pooled S peptides. Red
bars reflect median responses.

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Fig. 4. Viral loads in rhesus macaques challenged with SARS-CoV-2 virus. Rhesus macaques were challenged
by the intranasal and intratracheal route with 1.2 × 108 VP (1.1 × 104 PFU) SARS-CoV-2. (A) Log10 sgmRNA
copies/ml or copies/swab (limit 50 copies) were assessed in bronchoalveolar lavage (BAL) and nasal swabs
(NS) in sham controls at multiple timepoints following challenge. (B) Log10 sgmRNA copies/ml in BAL and (C)
log10 sgmRNA copies/swab in NS in vaccinated animals at multiple timepoints following challenge. (D) Summary
of peak viral loads in BAL and NS following challenge. Peak viral loads occurred variably on day 1-4 following
challenge. Red lines reflect median viral loads. P-values indicate two-sided Mann-Whitney tests.

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Fig. 5. Immune correlates of protection. Correlations of (A) pseudovirus NAb titers and (B) live NAb titers prior to
challenge with log peak sgmRNA copies/ml in BAL or log peak sgmRNA copies/swab in nasal swabs following
challenge. Red lines reflect the best-fit relationship between these variables. P and R values reflect two-sided
Spearman rank-correlation tests. (C) The heat map (top panel) shows the Spearman and Pearson correlations
between antibody features and log10 peak sgmRNA copies/ml in BAL (*q < 0.05, **q < 0.01, ***q < 0.001 with
Benjamini-Hochberg correction for multiple testing). The bar graph (bottom left panel) shows the rank of the
Pearson correlation between cross-validated model predictions and data using the most predictive combination or
individual antibody features for partial least square regression (PLSR) and random forest regression (RFR). The
correlation heatmap (bottom right panel) represents pairwise Pearson correlations between features across all
animals. (D) The heat map (top panel) shows the difference in the means of the z-scored features between the
completely protected and partially protected animals (**q < 0.01 with Benjamini-Hochberg correction for multiple
testing). The dot plots show differences in log10 NAb titers, RBD-specific ADCD responses, S-specific ADCD
responses, and RBD-specific ADCP responses between the completely protected and partially protected animals. P-
values indicate two-sided Mann-Whitney tests.

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DNA vaccine protection against SARS-CoV-2 in rhesus macaques
Jingyou Yu, Lisa H. Tostanoski, Lauren Peter, Noe B. Mercado, Katherine McMahan, Shant H. Mahrokhian, Joseph P. Nkolola,
Jinyan Liu, Zhenfeng Li, Abishek Chandrashekar, David R. Martinez, Carolin Loos, Caroline Atyeo, Stephanie Fischinger, John S.
Burke, Matthew D. Slein, Yuezhou Chen, Adam Zuiani, Felipe J. N. Lelis, Meghan Travers, Shaghayegh Habibi, Laurent Pessaint,
Alex Van Ry, Kelvin Blade, Renita Brown, Anthony Cook, Brad Finneyfrock, Alan Dodson, Elyse Teow, Jason Velasco, Roland
Zahn, Frank Wegmann, Esther A. Bondzie, Gabriel Dagotto, Makda S. Gebre, Xuan He, Catherine Jacob-Dolan, Marinela Kirilova,
Nicole Kordana, Zijin Lin, Lori F. Maxfield, Felix Nampanya, Ramya Nityanandam, John D. Ventura, Huahua Wan, Yongfei Cai, Bing
Chen, Aaron G. Schmidt, Duane R. Wesemann, Ralph S. Baric, Galit Alter, Hanne Andersen, Mark G. Lewis and Dan H. Barouch

published online May 20, 2020

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